Dissertations / Theses on the topic 'Founder events'

Doctor of Philosophy(PhD),
Until recently, Northwestern Australia was thought to be relatively free of serious fruit fly pests. Although a noxious strain, present in Darwin since 1985, was widely believed to be an infestation of the Queensland fruit fly, Bactrocera tryoni, from the East coast, the fruit flies present outside this area were believed to be the benign endemic species, B. aquilonis. However, during the year 2000, infestations of fruit flies were discovered on major commercial crops in both Western Australia and the Northern Territory. It was not known whether these outbreaks were due to an invasion of the major pest species, Bactrocera tryoni, a change in the behaviour of B. aquilonis, or a hybridisation event between the two species. Finding the source of these outbreaks has been complicated by the fact that, since B. tryoni and B. aquilonis are virtually indistinguishable morphologically, it was not known which species are present in the region. Traditionally any tryoni complex fly caught in the Northwest was called B. aquilonis based solely on location. In order to get a good population profile of the region, an extensive trapping program was set up to include flies from urban areas, commercial crops and natural areas where the benign strain is thought to remain. Tests of genetic differentiation and clustering analyses revealed a high degree of homogeneity in the Northwest samples, suggesting that just one species is present in the region. The Northwest samples were genetically differentiated from the Queensland samples but only to a small degree (FST =0.0153). MtDNA sequencing results also showed a small degree of differentiation between these regions. A morphological study of wing shape indicated that there are some minor identifiable morphological differences between East coast and Northwest laboratory reared flies. This difference was greater than that seen between B. jarvisi populations across the same geographic range. The results suggest that the flies caught in the Northwest are a separate population of B. tryoni. Soon after pest flies were discovered in Darwin, a population became established in Alice Springs. This population had a low genetic diversity compared with Queensland and Darwin populations, and showed evidence of being heavily founded. In 2000, an outbreak was discovered in the nearby town of Ti Tree. Due to the geographic and genetic similarity of these populations, Alice Springs was determined to be the source of the Ti Tree outbreak. To investigate the founding of these populations, a program was developed to estimate the propagule size. Using a simulation method seven different statistics were tested for estimating the propagule size of an outbreak population. For outbreaks originating from populations with high genetic diversity, the number of alleles was a good estimator of propagule size. When, however, the genetic diversity of the source population was already reduced, allele frequency measures, particularly the likelihood of obtaining the outbreak population from the source population, gave more accurate estimates. Applying this information to the Alice Springs samples, it was estimated that just five flies were needed to found the major population in and around Alice Springs. For Ti Tree, the propagule size was estimated to be 27 flies (minimum 10). In 2000, a much larger outbreak occurred in the developing horticultural region of Kununurra in northern Western Australia. An important question for the management of the problem is whether there is an established fly population or the flies are reinvading each year. This population was found to have a large amount of gene flow from the Northern Territory. Within the Kununurra samples, one group of flies was genetically differentiated from all the other samples. This group came from a small geographic area on the periphery of Kununurra and appeared to be the result of an invasion into this area at the time when the population was building up following the dry season. A further threat to the Northwest horticultural regions comes from B. jarvisi. A recent increase in the host range of this species has lead to speculation that it may become a greater pest in Northwestern Australia. At the present time, protocols for the population monitoring and disinfestation of this species are not in place. Here it is shown that B. jarvisi eggs are more heat tolerant than B. tryoni eggs and that monitoring of B. jarvisi populations is possible using cue lure traps placed according to fruiting time and location of their favoured host, Planchonia careya.

Until recently, Northwestern Australia was thought to be relatively free of serious fruit fly pests. Although a noxious strain, present in Darwin since 1985, was widely believed to be an infestation of the Queensland fruit fly, Bactrocera tryoni, from the East coast, the fruit flies present outside this area were believed to be the benign endemic species, B. aquilonis. However, during the year 2000, infestations of fruit flies were discovered on major commercial crops in both Western Australia and the Northern Territory. It was not known whether these outbreaks were due to an invasion of the major pest species, Bactrocera tryoni, a change in the behaviour of B. aquilonis, or a hybridisation event between the two species. Finding the source of these outbreaks has been complicated by the fact that, since B. tryoni and B. aquilonis are virtually indistinguishable morphologically, it was not known which species are present in the region. Traditionally any tryoni complex fly caught in the Northwest was called B. aquilonis based solely on location. In order to get a good population profile of the region, an extensive trapping program was set up to include flies from urban areas, commercial crops and natural areas where the benign strain is thought to remain. Tests of genetic differentiation and clustering analyses revealed a high degree of homogeneity in the Northwest samples, suggesting that just one species is present in the region. The Northwest samples were genetically differentiated from the Queensland samples but only to a small degree (FST =0.0153). MtDNA sequencing results also showed a small degree of differentiation between these regions. A morphological study of wing shape indicated that there are some minor identifiable morphological differences between East coast and Northwest laboratory reared flies. This difference was greater than that seen between B. jarvisi populations across the same geographic range. The results suggest that the flies caught in the Northwest are a separate population of B. tryoni. Soon after pest flies were discovered in Darwin, a population became established in Alice Springs. This population had a low genetic diversity compared with Queensland and Darwin populations, and showed evidence of being heavily founded. In 2000, an outbreak was discovered in the nearby town of Ti Tree. Due to the geographic and genetic similarity of these populations, Alice Springs was determined to be the source of the Ti Tree outbreak. To investigate the founding of these populations, a program was developed to estimate the propagule size. Using a simulation method seven different statistics were tested for estimating the propagule size of an outbreak population. For outbreaks originating from populations with high genetic diversity, the number of alleles was a good estimator of propagule size. When, however, the genetic diversity of the source population was already reduced, allele frequency measures, particularly the likelihood of obtaining the outbreak population from the source population, gave more accurate estimates. Applying this information to the Alice Springs samples, it was estimated that just five flies were needed to found the major population in and around Alice Springs. For Ti Tree, the propagule size was estimated to be 27 flies (minimum 10). In 2000, a much larger outbreak occurred in the developing horticultural region of Kununurra in northern Western Australia. An important question for the management of the problem is whether there is an established fly population or the flies are reinvading each year. This population was found to have a large amount of gene flow from the Northern Territory. Within the Kununurra samples, one group of flies was genetically differentiated from all the other samples. This group came from a small geographic area on the periphery of Kununurra and appeared to be the result of an invasion into this area at the time when the population was building up following the dry season. A further threat to the Northwest horticultural regions comes from B. jarvisi. A recent increase in the host range of this species has lead to speculation that it may become a greater pest in Northwestern Australia. At the present time, protocols for the population monitoring and disinfestation of this species are not in place. Here it is shown that B. jarvisi eggs are more heat tolerant than B. tryoni eggs and that monitoring of B. jarvisi populations is possible using cue lure traps placed according to fruiting time and location of their favoured host, Planchonia careya.

Background: We aimed to increase the knowledge regarding the familial arrhythmogenic disorder Long QT Syndrome (LQTS) and its recessive variant Jervell and Lange-Nielsen Syndrome (JLNS) in Sweden, including prevalences and clinical phenotypes. A specific focus was directed towards two KCNQ1 mutations –p.Y111C and p.R518X- commonly identified in Swedish LQTS index cases. Methods: Cases and families with LQTS (p.Y111C or p.R518X) and JLNS were recruited via regional clinical practices, national referrals to the Clinical Genetics laboratory, Umeå University Hospital, and a national inventory. Molecular genetics methods were used for case ascertainment. Clinical data was obtained via medical records, a questionnaire, and/or an interview. Electrocardiograms were manually assessed. In p.R518X heterozygotes intra-familial phenotypic variability (QTc and cardiac events) was assessed by analysis of sequence variants (modifier genes). The origins of the mutations p.Y111C and p.R518X were investigated using genealogical and haplotype analysis (microsatellite markers). In families sharing a common haplotype mutation age and associated prevalence was analyzed using ESTIAGE and DMLE computer software. Results: We identified p.Y111C (170 mutation-carriers) and p.R518X (101 mutation-carriers) as two major causes of LQTS/JLNS in Sweden. LQTS phenotype was revealed to be relatively benign in p.Y111C and p.R518X (annual incidence of life-threatening cardiac events, before therapy 0.05% and 0.04%, respectively). Gender-specific effects of genetic modifiers on phenotypic expression were seen. A founder origin, approximately 600-700 years ago in two northern river valleys was established for p.Y111C and p.R518X, and a high prevalence of LQTS founder descendants suggested. A minimum JLNS prevalence of 1:200 000 in preadolescent Swedish children was revealed. JLNS phenotype was mainly severe, with a cumulative incidence of life-threatening cardiac events of 53% (annual incidence rate before therapy 5%) and four sudden deaths. Possible founder effects regarding four KCNQ1 mutations; p.Y111C (8%), p.R518X (50%), c.572_576del (17%) and p.Q530X (8%) together explained 83% of the JLNS mutation-spectrum in Sweden, consisting of 8 KCNQ1 mutations. Conclusion: The high prevalence of p.Y111C- and p.R518X-related LQTS as well as JLNS revealed in Sweden could be explained by the combination of mild clinical phenotypes in heterozygotes and strong founder effects present during the population development of northern Sweden. Increased knowledge regarding the occurrence of LQTS and JLNS as well as mutation- and/or genotype-specific data constitute prerequisites for possible improvement of patient management.

Historical biogeography has a diversity of methods for inferring ancestral geographic ranges on phylogenies, but many of the methods have conflicting assumptions, and there is no common statistical framework by which to judge which models are preferable. Probabilistic modeling of geographic range evolution, pioneered by Ree and Smith (2008, Systematic Biology) in their program LAGRANGE, could provide such a framework, but this potential has not been implemented until now.

I have created an R package, "BioGeoBEARS," described in chapter 1 of the dissertation, that implements in a likelihood framework several commonly used models, such as the LAGRANGE Dispersal-Extinction-Cladogenesis (DEC) model and the Dispersal-Vicariance Analysis (DIVA, Ronquist 1997, Systematic Biology) model. Standard DEC is a model with two free parameters specifying the rate of "dispersal" (range expansion) and "extinction" (range contraction). However, while dispersal and extinction rates are free parameters, the cladogenesis model is fixed, such that the geographic range of the ancestral lineage is inherited by the two daughter lineages through a variety of scenarios fixed to have equal probability. This fixed nature of the cladogenesis model means that it has been indiscriminately applied in all DEC analyses, and has not been subjected to any inference or formal model testing.

BioGeoBEARS also adds a number of features not previously available in most historical biogeography software, such as distance-based dispersal, a model of imperfect detection, and the ability to include fossils either as ancestors or tips on a time-calibrated tree.

Several important conclusions may be drawn from this research. First, formal model selection procedures can be applied in phylogenetic inferences of historical biogeography, and the relative importance of different processes can be measured. These techniques have great potential for strengthening quantitative inference in historical biogeography. No longer are biogeographers forced to simply assume, consciously or not, that some processes (such as vicariance or dispersal) are important and others are not; instead, this can be inferred from the data. Second, founder-event speciation appears to be a crucial explanatory process in most clades, the only exception being some intracontinental taxa showing a large degree of sympatry across widespread ranges. This is not the same thing as claiming that founder-event speciation is the only important process; founder event speciation as the only important process is inferred in only one case (Microlophus lava lizards from the Galapagos). The importance of founder-event speciation will not be surprising to most island biogeographers. However, the results are important nonetheless, as there are still some vocal advocates of vicariance-dominated approaches to biogeography, such as Heads (2012, Molecular Panbiogeography of the Tropics), who allows vicariance and range-expansion to play a role in his historical inferences, but explicitly excludes founder-event speciation a priori. The commonly-used LAGRANGE DEC and DIVA programs actually make assumptions very similar to those of Heads, even though many users of these programs likely consider themselves dispersalists or pluralists. Finally, the inclusion of fossils and imperfect detection within the same likelihood and model-choice framework clears the path for integrating paleobiogeography and neontological biogeography, strengthening inference in both.

Model choice is now standard practice in phylogenetic analysis of DNA sequences: a program such as ModelTest is used to compare models such as Jukes-Cantor, HKY, GTR+I+G, and to select the best model before inferring phylogenies or ancestral states. It is clear that the same should now happen in phylogenetic biogeography. BioGeoBEARS enables this procedure. Perhaps more importantly, however, is the potential for users to create and test new models. Probabilistic modeling of geographic range evolution on phylogenies is still in its infancy, and undoubtedly there are better models out there, waiting to be discovered. It is also undoubtedly true that different clades and different regions will favor different processes, and that further improvements will be had by linking the evolution of organismal traits (e.g., loss of flight) with the evolution of geographic range, within a common inference framework. In a world of rapid climate change and habitat loss, biogeographical methods must maximize both flexibility and statistical rigor if they are to play a role. This research takes several steps in that direction.

BioGeoBEARS is open-source and is freely available at the Comprehensive R Archive Network (http://cran.r-project.org/web/packages/BioGeoBEARS/index.html). A step-by-step tutorial, using the Psychotria dataset, is available at PhyloWiki (http://phylo.wikidot.com/biogeobears).

(Abstract shortened by UMI.)

Selection and genetic drift are often competing forces in shaping genetic structure in populations. Genetic drift will often effectively cancel out the effect of selection when population sizes are small, such as in colonizing island populations. On a small island in the Skeppsvik Archipelago in northern Sweden, a newly founded population of Silene dioica has been monitored since it first established around 1993. Though inhabiting an area of merely 173 m2, the population has been shown to exhibit a genetically differentiated patch structure where closely related individuals are tightly grouped, distanced from other family groups. In this study, the effect of selection was evaluated as compared to that of genetic drift. Variation in phenotypic traits in flowers, leaves and stalks were compared to that of neutral markers, in the form of PST and FST measures, to assess a measure of what proportion of differentiation among patches in phenotypic traits could not be attributed to genetic drift. Males and females were analysed separately to obtain measures of sex specific selection. Signs of divergent and stabilizing selection were found in several traits in both males and females despite the small spatial scale and short time since colonization. Further analysis is needed to assess explanations for trait divergence among patches and direction of selection.

This thesis offers an ethnography, with both audiovisual and written components, of the virtual places brought into being through the creation and consumption of event videos in a transnational community. It is intended as a contribution to the development of conceptual and methodological frameworks, which will allow anthropological engagements with vernacular audiovisual media that take into account their phenomenological properties as mimetically active assemblages. In San Francisco Tetlanohcan, Mexico, young parents often leave their children behind as they cross the border illegally, heading north to look for work. Event videos, made by videographers at rite of passage ceremonies and sent to the USA, are an important aspect of migrant life. This research draws on thinking in philosophy and film studies to conceptualise these videos as agents in a process of ‘filmic emplacement’ as their production and consumption bring into being imagined places and selves. The project combines methodological approaches borrowed from sensory ethnography with video editing techniques inspired by avant-garde filmmaking, in a dynamic evocation and exploration of these filmic places. Close participation in the creation and consumption of event videos combined with the movement of alternative ‘video messages’ across the border, gave the researcher a sense of these places. Shared screenings of found footage sequences materialised and refined that understanding. By co-opting the aesthetics of popular television, event videos transform that which they depict, bringing into being collectively created and experienced imagined places. This coherent and constant virtual realm allows for the creation and maintenance of kinship and fictive kinship relationships, despite separations over space and time. The video 900,000 Frames Between Us produced as part of this thesis uses the juxtaposition of ontologically diverse images and sounds to provide an audiovisual evocation of this ‘filmic home’. In addition to contributing to the anthropological understanding of San Francisco, this thesis suggests ways in which visual anthropologists might engage with and understand the mediated experiences of others.

Osteoarthritis (OA) is a common musculoskeletal disease, associated with significant cost to the National Health Service (NHS) and physical consequences to the sufferer. It is known that cartilage degradation and subchondral sclerosis are hallmark features of OA. However, it is not known in which tissue pathological changes occur first. By identifying this, future therapeutics could be guided more accurately to maximise their benefit. This study has highlighted significant problems in generating a reliable and reproducible human‐derived model of cartilage catabolism using human mesenchymal stem cells (hMSCs). Generating such a model is important, as it will allow assessment of potential therapies in a physiologically relevant human model, and further work is needed in this area. However, one significant finding from this work was that the addition of matriptase to a cytokine stimulus enhanced proteoglycan and collagen degradation from cartilage discs and macro‐pellets. Matriptase is a serine proteinase, and is involved in cartilage catabolism through activation of pro‐MMPs and signaling via PAR‐2. These findings therefore support the role of matriptase in OA pathogenesis, specifically cartilage catabolism. Proteinase‐activated receptor‐2 (PAR‐2) is known to be involved in OA pathogenesis, with global ablation of this receptor preventing abnormal remodelling events in the cartilage and subchondral bone. In this study, tissue‐specific ablation of PAR‐2 revealed that loss of PAR‐2 conferred its primary beneficial effect in the bone by preventing subchondral sclerosis. The debate about whether cartilage or bone changes occur first in OA remains controversial, but it was apparent from various time‐course studies that bone changes occurred first, followed by cartilage catabolism during OA progression. However, in this study it was also evident that cartilage damage could occur independently of subchondral sclerosis, which is in opposition to the long standing view that subchondral sclerosis is a prerequisite for cartilage damage to occur. Thus, this study highlights that targeting either the cartilage or bone may be beneficial for therapies, although for ease of use, targeting the bone may be more clinically useful. Furthermore the importance of PAR‐2 expressed on chondrocytes in the development and maturation of osteophytes was evident in this study.

La tesi que teniu a les mans recull quatre treballs amb un objectiu comú; determinar si els patògens (virus, bacteris, paràsits.) han exercit pressions selectives sobre els genomes dels seus hostes (com per exemple els humans).
Sabent que la detecció de l'empremta de la selecció permet identificar aquelles regions del genoma que han estat rellevants al llarg de l'evolució d'una espècie, ja que a nivell local és la variació funcional qui acaba essent objecte de la selecció, ens hem disposat a estudiar els possibles senyals de selecció en gens relacionats amb la interacció hoste-patògen. En concret, hem analitzat gens que codifiquen per: a) components del sistema immunitari innat i, b) enzims de glicosilació, la majoria dels quals s'inclouen en quatre de les principals rutes biosintètiques de glicans, en diferents poblacions humanes.
Com a conclusió principal; ambdós conjunts de gens mostren clars senyals de selecció. A més hem vist que segons el context biològic on és troben certs gens és veuen més afectats per l'acció de la selecció natural.
The present thesis includes four studies with a common objective: determining whether pathogens (virus, bacteria, parasites.) have exerted selective pressures on the genome of their hosts (for example, humans).
Detecting signatures of positive selection is a useful tool to identify functionally relevant genomic regions since selection locally shapes the functional variation. Based on this premise, we have studied the possible signatures of selection in genes related to host-pathogen interactions. Specifically, we have analyzed those genes encoding: a) components of the innate immunity response; and ii) glycosylation enzymes most of them involved in four major glycan biosynthesis pathways, in different human populations.
The main conclusion obtained from these studies is that both studied gene categories show clear signatures of selection. Moreover, we have determined that according to their biological context certain genes are more prone to the action of selection.

No Fault Founds (NFFs) are an expensive problem faced by the airline industry. The underlying cause of NFFs are a major focus of research work in the field, but the dearth of consistent data is a roadblock faced by many decision makers. An important risk factor identified is the occurrence rate of NFFs.

This research work aims to help decision makers in the Airline Maintenance, Repair and Overhaul teams, when faced with recurring NFFs, to make a choice based on value derived from the system and risk preference of the decision maker under uncertainty. The value of the aircraft fleet is laid out using Net Present Value at every decision point along the system life cycle while accounting for the uncertainty in the failure rate information. Two extreme decisions are considered for the decision maker to choose between: rebooting the system every time a failure occurs and results in an NFF which allows for it to recur while reducing uncertainty of the failure rate; or eliminating the failure mode which assumes that the failure does not recur and therefore completely removes the uncertainty. Both decisions have their associated uncertain costs that affect the NPV calculated. We use a Monte Carlo approach to estimate the expected profit from deciding to eliminate the failure mode. We make use of Expected Utility Theory to account for the risk preference of a decision maker under uncertainty and build an Expected Utility Maximizing decision framework.

To conclude we give some guidance to interpret the results and understand what factors influence the optimal decision. We conclude that not accounting for uncertainty in estimating a failure rate for the future along with uncertainty in NFF costs can lead to an undesirable decision. If the decision maker waits too long to gather more information and reduce uncertainty, then rebooting the system for the remaining life could be more worthwhile than spending the large amount of money to Eliminate a failure mode. Finally, we conclude that, despite uncertainties in information of occurrence rates and costs of NFFs, an Expected Utility maximizing decision between the two options considered – Reboot and Eliminate – is possible given the available information.

碩士
國立交通大學
工學院碩士在職專班產業安全與防災組
96
High-tech industry has been viewed as the lead industry in Taiwan. The semiconductor industry is also an indicator of current economic development and is listed as “Two Trillion and Twin Star Industries Development Plan” by Executive Yuan. The output value of the semiconductor industry in Taiwan is estimated to 1.7 trillions and will hit the all-time high in 2008. However, the environment protection has been awakened and the problem on flare gas or waste liquid derived from the production process of semi-conductor has been taken seriously along with the issue on global warming. The local scrubber equipment is one of the important parts of the production process. There have been many researches on the processing efficiency other than the risk assessment of the local scrubber equipment. Accordingly, this research is sampling on the abnormal events of local scrubber in some foundry to examine the safe design of the equipment and to reduce the condition of the damage. We made the initial evaluation with regard to the damage and found out the relative degree of the damage for each unit. The result showed that the identity of the local scrubber and its piping were under relative high risk of damage. For high potential risk of damage, we used “Hazard And Operation Study” to analyze the damage factors and focus on the issue on improvement, especially on action plan of engineering control. Finally, we compared the abnormal events occurred during the year when the action plan is implemented with last year when no action plan was carried out. Then it was resulted that action plan was actually efficiently reduced the degree of the damage for the system risk. This method can be carried into effect for further expansion and to provide a safe environment for the operators.

abstract: This thesis describes the design of a Single Event Transient (SET) duration measurement test-structure on the Global Foundries (previously IBM) 32-nm silicon-on insulator (SOI) process. The test structure is designed for portability and allows quick design and implementation on a new process node. Such a test structure is critical in analyzing the effects of radiation on complementary metal oxide semi-conductor (CMOS) circuits. The focus of this thesis is the change in pulse width during propagation of SET pulse and build a test structure to measure the duration of a SET pulse generated in real time. This test structure can estimate the SET pulse duration with 10ps resolution. It receives the input SET propagated through a SET capture structure made using a chain of combinational gates. The impact of propagation of the SET in a >200 deep collection structure is studied. A novel methodology of deploying Thick Gate TID structure is proposed and analyzed to build multi-stage chain of combinational gates. Upon using long chain of combinational gates, the most critical issue of pulse width broadening and shortening is analyzed across critical process corners. The impact of using regular standard cells on pulse width modification is compared with NMOS and/or PMOS skewed gates for the chain of combinational gates. A possible resolution to pulse width change is demonstrated using circuit and layout design of chain of inverters, two and three inputs NOR gates. The SET capture circuit is also tested in simulation by introducing a glitch signal that mimics an individual ion strike that could lead to perturbation in SET propagation. Design techniques and skewed gates are deployed to dampen the glitch that occurs under the effect of radiation. Simulation results, layout structures of SET capture circuit and chain of combinational gates are presented.
Dissertation/Thesis
Masters Thesis Electrical Engineering 2017